Crystal structure of yellow fever virus NS3 helicase

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 

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This is version 1.3 of the entry. See complete history


Structure of the flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing.

Wu, J.Bera, A.K.Kuhn, R.J.Smith, J.L.

(2005) J Virol 79: 10268-10277

  • DOI: https://doi.org/10.1128/JVI.79.16.10268-10277.2005
  • Primary Citation of Related Structures:  
    1YKS, 5FFM

  • PubMed Abstract: 

    Yellow fever virus (YFV), a member of the Flavivirus genus, has a plus-sense RNA genome encoding a single polyprotein. Viral protein NS3 includes a protease and a helicase that are essential to virus replication and to RNA capping. The 1.8-A crystal structure of the helicase region of the YFV NS3 protein includes residues 187 to 623. Two familiar helicase domains bind nucleotide in a triphosphate pocket without base recognition, providing a site for nonspecific hydrolysis of nucleoside triphosphates and RNA triphosphate. The third, C-terminal domain has a unique structure and is proposed to function in RNA and protein recognition. The organization of the three domains indicates that cleavage of the viral polyprotein NS3-NS4A junction occurs in trans.

  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein [contains: Flavivirin protease NS3 catalytic subunit]440Yellow fever virusMutation(s): 0 
Find proteins for P03314 (Yellow fever virus (strain 17D vaccine))
Explore P03314 
Go to UniProtKB:  P03314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03314
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.018α = 90
b = 43.801β = 104
c = 93.069γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references